Rare soil organisms are normally considered of less importance for ecosystem functioning. We present results that oppose this view. In otherwise well-aerated soils, anaerobic/microaerophilic production or consumption of the trace gas N2O occurs in small soil volumes, when intense decomposition activity at the site leads to local oxygen depletion. At such patch scales, the control of microbial growth and oxygen consumption may depend on the specific organisms present. We assessed N2O turnover in an experiment, where soil dilution from 10−2 over 10−4 to 10−6 followed by microbial regrowth resulted in similar microbial biomass and respiration but reduced diversity. We found an increasing number of very high N2O turnover rates when soil dilution increased from 10−2 over 10−4 to 10−6, as revealed from a significantly increased skewness of the frequency distribution of N2O turnover levels. N2O turnover also tended to increase (p = 0.08) by 20–30% when soil was diluted from 10−2 to 10−6. This suggests that rare soil organisms regulate the local activity of fast-growing microorganisms and thus reduce the probability that anoxic/microaerophilic soil volumes develop. Future studies may reveal which less abundant organisms prevent development of anoxic/microaerophilic conditions in well-aerated soils.